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- PDB-1ba3: FIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM -

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Basic information

Entry
Database: PDB / ID: 1ba3
TitleFIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM
ComponentsLUCIFERASE
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / PHOTOPROTEIN / LUMINESCENCE
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIBROMOMETHANE / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFranks, N.P. / Jenkins, A. / Conti, E. / Lieb, W.R. / Brick, P.
Citation
Journal: Biophys.J. / Year: 1998
Title: Structural basis for the inhibition of firefly luciferase by a general anesthetic.
Authors: Franks, N.P. / Jenkins, A. / Conti, E. / Lieb, W.R. / Brick, P.
#1: Journal: Embo J. / Year: 1997
Title: Structural Basis for the Activation of Phenylalanine in the Non-Ribosomal Biosynthesis of Gramicidin S
Authors: Conti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P.
#2: Journal: Structure / Year: 1996
Title: Crystal Structure of Firefly Luciferase Throws Light on a Superfamily of Adenylate-Forming Enzymes
Authors: Conti, E. / Franks, N.P. / Brick, P.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Diffraction Studies of Firefly Luciferase from Photinus Pyralis
Authors: Conti, E. / Lloyd, L.F. / Akins, J. / Franks, N.P. / Brick, P.
History
DepositionApr 21, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LUCIFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3243
Polymers60,8191
Non-polymers5052
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.560, 119.560, 95.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LUCIFERASE


Mass: 60818.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli (E. coli) / References: UniProt: P08659, firefly luciferase
#2: Chemical ChemComp-MBR / TRIBROMOMETHANE


Mass: 252.731 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHBr3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 283 K / Method: microbatch under oil / pH: 7.8
Details: 2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG ...Details: 2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL., microbatch under oil, temperature 283K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion
Details: Conti, E., (1996) Acta Crystallogr.,Sect.D, 52, 876.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2200 mMammonium sulfate1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
510 %glycerol1drop
625 %ethylene glycol1drop
725 mMTris1drop
8500-540 mMlithium sulfate1reservoir
926 %(w/v)PEG80001reservoir
10100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 1997 / Details: MIRRORS
RadiationMonochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→18.4 Å / Num. obs: 35038 / % possible obs: 98.2 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.235 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 109681
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCI

1lci


Resolution: 2.2→18.4 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1737 5 %RANDOM
Rwork0.197 ---
obs0.197 35006 97.9 %-
Displacement parametersBiso mean: 29.9 Å2
Refine analyzeLuzzati d res low obs: 18.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 8 353 4491
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.261.5
X-RAY DIFFRACTIONx_mcangle_it3.422
X-RAY DIFFRACTIONx_scbond_it3.542
X-RAY DIFFRACTIONx_scangle_it4.832.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 223 5 %
Rwork0.29 223 -
obs--97.11 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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